According to the aide, the request was made "without authorization" and the staffer, who is no longer with the team, "overstepped his boundaries."
Sources say the request was not made by the president-elect.
Reports surfaced in recent days that the transition team had requested clearances for Ivanka, Donald Jr. and Eric and raised eyebrows because they will likely be running their fathers' businesses while he is in office.
Meanwhile, the transition team overcame a stumbling block Tuesday night after signing a memorandum of understanding with the White House that put Vice President-elect Mike Pence in charge.
"The next step is for the President-elect's transition team to provide us with the names of the individuals they have authorized to represent their transition effort across the government," White House spokesperson Brandi Hoffine said. "Once we have received those names and related materials, those individuals will be able to receive the briefing materials we have prepared and begin to communicate with their Obama Administration agency counterparts as we continue our work to facilitate the transition to the next Administration."
The memo is required by law.